SAXSdb — 1vrb

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Putative asparaginyl hydroxylase

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FE (III) ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FE (III) ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YXBC_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–342； UniProt 1–330 Author chain B； PDBConstruct 13–342； UniProt 1–330 Author chain C； PDBConstruct 13–342； UniProt 1–330 Author chain D； PDBConstruct 13–342； UniProt 1–330

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1vrb
Deposition date deposition_date	2005-02-18
Structure title title	Crystal structure of Putative asparaginyl hydroxylase (2636534) from Bacillus subtilis at 2.60 A resolution
Keywords keywords	;2636534, putative asparaginyl hydroxylase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, OXIDOREDUCTASE ;; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1vrb__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1vrb__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vrb__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	26.73 Å
Rg (electron density)	25.77 Å
Total Rg	26.61 Å
Atom count	4506
Residues	601
Excluded volume	80808 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vrb__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vrb__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Putative asparaginyl hydroxylase
Molecular weight formula_weight	39283.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9036

MGSDKIHHHHHHMSAVTESVLESIISPVTMSEFLEEYWPVKPLVARGEVERFTSIPGFEKVRTLENVLAIYNNPVMVVGDAVIEESEGITDRFLVSPAEALEWYEKGAALEFDFTDLFIPQVRRWIEKLKAELRLPAGTSSKAIVYAAKNGGGFKAHFDAYTNLIFQIQGEKTWKLAKNENVSNPMQHYDLSEAPYYPDDLQSYWKGDPPKEDLPDAEIVNLTPGTMLYLPRGLWHSTKSDQATLALNITFGQPAWLDLMLAALRKKLISDNRFRELAVNHQSLHESSKSELNGYLESLIQTLSENAETLTPEQIFQSQDSDFDPYQSTQLVFRQLLTSYKF

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	22

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1vrba1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.11 — Asparaginyl hydroxylase-like

Domain ID domain_id	d1vrbb_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.11 — Asparaginyl hydroxylase-like

Domain ID domain_id	d1vrbc_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.11 — Asparaginyl hydroxylase-like

Domain ID domain_id	d1vrbd_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.11 — Asparaginyl hydroxylase-like

CATH v4.4 (8 domains)

Domain ID domain_id	1vrbA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	1vrbA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1vrbB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	1vrbB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1vrbC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	1vrbC02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1vrbD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	1vrbD02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	47.300 Å
Unit-cell length b length_b	104.660 Å
Unit-cell length c length_c	286.610 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	28.660 Å
R factor r_factor	0.2240
R_work r_work	0.2214
R_free r_free	0.2723

Crystal structure of Putative asparaginyl hydroxylase (2636534) from Bacillus subtilis at 2.60 A resolution

1. Protein Identity and Related Structures Protein Identity & Related Structures

Putative asparaginyl hydroxylase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1vrb__assembly_2__model_1

1vrb__assembly_2__model_1 | I(q)

1vrb__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of Putative asparaginyl hydroxylase (2636534) from Bacillus subtilis at 2.60 A resolution

1. Protein Identity and Related Structures Protein Identity & Related Structures

Putative asparaginyl hydroxylase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1vrb__assembly_2__model_1

1vrb__assembly_2__model_1 | I(q)

1vrb__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)